Crystal structure of human cytochrome P450 2B6 (Y226H/K262R) in complex with an analog of a drug efavirenz

Structure

x-ray diffraction · 2 distinct chains · 51% helix, 9% strand (DSSP).

Ligands and binding sites

• HEM · Protoporphyrin IX containing Fe · ligand · 6 copies · chains A, B, C, D, E, F
• 9ZJ · (2R,4S)-6-chloro-4-(cyclopropylethynyl)-2-methyl-4-(trifluoromethyl)-1,4-dihydro-2H-3,1-benzoxazine · ligand · 6 copies · chains A, B, C, D, E, F
• CM5 · 5-cyclohexyl-1-pentyl-beta-D-maltoside · ligand · 5 copies · chains B, C, D, E, F
• ZAZ · 5-cyclohexylpentan-1-ol · ligand · chains A

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

20 pockets found on a 1 Å grid, 18 with a druggability of 0.5 or more.

Interfaces

12 interfaces between chains.

• B–C · 512 Ų buried · 3 hydrogen bonds · protein-protein
• A–C · 511 Ų buried · 4 hydrogen bonds · protein-protein
• D–F · 490 Ų buried · 4 hydrogen bonds · protein-protein
• D–E · 484 Ų buried · 4 hydrogen bonds · protein-protein
• E–F · 484 Ų buried · 6 hydrogen bonds · protein-protein

Compared structures

• 5WBG · Crystal Structure of human Cytochrome P450 2B6 (Y226H/K262R) in complex with an analog of… · the same entry in another collection · chain F against F, TM-score 1.00
• P20813 · AlphaFold monomer V2.0 prediction for cytochrome P450 2B6 (P20813) · a predicted model of the same protein · chain E against A, TM-score 0.99

Analyse

• Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
• Every structure of UniProt P20813
• Elsewhere: RCSB PDB 5WBG · PDBe 5WBG · UniProt P20813